TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv0604/lpqO:

update plot	correlation	link to info on gene
Rv2879c/-	(cc=0.519)	info on Rv2879c/-
Rv1249c/-	(cc=0.4964)	info on Rv1249c/-
Rv1442/bisC	(cc=0.4954)	info on Rv1442/bisC
Rv3532/PPE61	(cc=0.4866)	info on Rv3532/PPE61
Rv0302/-	(cc=0.4756)	info on Rv0302/-
Rv2007c/fdxA	(cc=0.4718)	info on Rv2007c/fdxA
Rv2880c/-	(cc=0.4691)	info on Rv2880c/-
Rv0015c/pknA	(cc=0.4678)	info on Rv0015c/pknA
Rv0269c/-	(cc=0.4656)	info on Rv0269c/-
Rv0061c/-	(cc=0.4604)	info on Rv0061c/-

Correlation of Rv0604/lpqO with Rv0269c/-

Normalized LFCs for Rv0604/lpqO:
(description and provenance of datasets)

	Rv0604/lpqO	Rv0269c/-
Fe_supp_jason_reseq	1.159	0.905
low_pH_jason_reseq	-1.474	-0.099
NO_jason_reseq	-2.195	0.029
B6_jason_reseq	0.798	1.569
MHCII_jason_reseq	1.287	1.229
Isoniazid02	0.038	0.012
Rifampicin4	0.347	0.333
Ethambutol3	-0.17	0.295
Meropenem3	0.048	0.054
Vancomycin16	0.0	-0.082
Rv2680_day32	-0.525	1.037
H37Rv_KO_MarP	0.116	0.574
hypoxia_3wks	0.53	0.199
hypoxia_6wks	-0.507	0.248
glycerol	1.27	-0.313
cholesterol	0.077	0.086
AJ	0.729	0.148
Bibs02	1.249	-0.293
Bibs02c	0.896	0.192
BL6	0.144	-0.227
BL6a	0.027	0.0
BXD01	0.39	0.006
BXD010	-0.118	-0.161
BXD011	-0.94	-0.453
BXD03	-0.115	-0.223
BXD04	-1.037	0.083
BXD05	0.089	-0.513
BXD06	-0.78	0.057
BXD07	-0.46	-0.201
BXD08	0.509	0.44
BXD09	-0.416	-0.102
CAST	-0.112	-0.03
CCcont	0.098	-0.286
DS01	0.731	0.373
DS02	0.684	0.767
DS04	0.839	0.025
DS0c	0.404	0.8
GP01	0.0	1.082
GP02	-0.262	-0.014
GP0c	-0.101	0.349
NOD	-0.921	-0.679
NZO	0.118	0.231
PWK	-0.124	0.06
H37Rv_KO_CtpC	-1.291	-0.111
H37Rv_KO_CtpD	-0.532	1.228
H37Rv_KO_Rv1272	-1.06	-0.248
H37Rv_KO_SugABC	-1.802	-0.687
H37Rv_KO_MbtN	-0.819	0.087
Trans05	0.462	0.575
macrophage_unactivated	1.18	-0.423
IL1	0.027	-0.522
Rapamycin	-0.792	0.068
Tcell	-0.274	0.098
GMCSF	0.14	0.0
IFNab	-0.342	-0.405
IFNg	-1.085	-0.38
IFNg_GMCSF1	2.124	1.125
Rv1432_day32	1.395	0.209
Rv1565c_day32	1.058	0.957
secA2_input	-0.221	0.16
delta_Rv3594	-0.857	-0.462
delta_Rv3717	-1.05	-0.773
delta_Rv3811	-1.689	-1.453
delta_Rv0954	-0.724	-0.474
PonA1	-2.328	0.38
EccD1_KO	0.506	0.355
EspI_KO	-0.24	-0.143
PE35_KO	0.175	0.198
PPE68_KO	0.637	-0.16
glycerol2	0.726	0.242
lignocerate	1.142	0.413
oleate	1.353	0.671
phosphatidylcholine	1.452	0.367
acetate	0.843	0.221
glucAc	0.631	0.302
Rv0950ko	0.799	0.259
Rv1096ko	0.124	0.739
Rv3684ko	0.665	0.629
delta_otsA_trehalose	1.318	0.272